Variant report

Variant	rs2872613
Chromosome Location	chr6:161520226-161520227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:161519466-161521806	K562	blood:	n/a	n/a

Variant related genes	Relation type
MAP3K4	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1001809	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754459	1.00[JPT][hapmap]
rs11963931	1.00[JPT][hapmap]
rs12195072	1.00[LWK][hapmap]
rs13194157	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464779	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1464780	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1543261	0.89[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562026	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1982291	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2275925	1.00[JPT][hapmap]
rs2275926	1.00[JPT][hapmap]
rs4472323	1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559074	1.00[ASN][1000 genomes]
rs4708898	0.82[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709486	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709489	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709490	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709491	0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709492	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4709493	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709495	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709496	1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587501	1.00[ASN][1000 genomes]
rs615269	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs619393	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs628430	1.00[ASN][1000 genomes]
rs628923	1.00[ASN][1000 genomes]
rs6455701	1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455703	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs645718	1.00[ASN][1000 genomes]
rs647923	0.84[TSI][hapmap]
rs657551	1.00[ASN][1000 genomes]
rs668638	1.00[ASN][1000 genomes]
rs682110	1.00[ASN][1000 genomes]
rs683549	1.00[ASN][1000 genomes]
rs6900500	1.00[JPT][hapmap]
rs6902332	1.00[ASN][1000 genomes]
rs6902760	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905942	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913706	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6914092	1.00[JPT][hapmap]
rs6918476	1.00[ASN][1000 genomes]
rs6919831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923835	1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap]
rs6925502	0.89[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6925800	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6929462	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6933810	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705829	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs705830	1.00[ASN][1000 genomes]
rs7738762	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7753585	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7760056	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346846	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9355330	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355332	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355867	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9355872	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355873	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9364585	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9364586	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365248	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9458126	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2872613	LOC729603	cis	cerebellum	SCAN
rs2872613	OSTCL	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161491000-161538400	Strong transcription	Primary B cells from peripheral blood	blood
2	chr6:161491600-161525400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:161491600-161528800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr6:161491600-161529000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:161491600-161539800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:161493800-161521400	Strong transcription	Fetal Thymus	thymus
7	chr6:161494400-161525600	Strong transcription	Dnd41	blood
8	chr6:161494400-161542400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr6:161495200-161538000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:161496000-161539800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:161497800-161539600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:161498000-161541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:161498600-161525600	Strong transcription	Primary T cells from cord blood	blood
14	chr6:161499000-161531800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:161499800-161521600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:161500200-161540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:161500400-161525600	Strong transcription	Adipose Nuclei	Adipose
18	chr6:161500600-161539800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr6:161500600-161541800	Strong transcription	K562	blood
20	chr6:161500800-161538200	Strong transcription	Primary B cells from cord blood	blood
21	chr6:161502600-161531600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:161503200-161532000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:161504800-161531800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr6:161505000-161524200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:161505000-161524400	Weak transcription	Psoas Muscle	Psoas
26	chr6:161505000-161528200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:161505800-161529800	Weak transcription	Fetal Brain Male	brain
28	chr6:161507000-161524000	Weak transcription	A549	lung
29	chr6:161509400-161528000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:161510000-161520800	Weak transcription	Hela-S3	cervix
31	chr6:161510600-161529000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:161510600-161531600	Weak transcription	Stomach Mucosa	stomach
33	chr6:161510800-161537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:161511800-161521400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:161512600-161528200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:161512800-161520800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr6:161513200-161523400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:161513600-161523000	Weak transcription	Fetal Heart	heart
39	chr6:161514000-161521200	Strong transcription	Fetal Kidney	kidney
40	chr6:161514000-161544600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:161514200-161525400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:161514400-161524600	Strong transcription	HSMM	muscle
43	chr6:161514400-161539800	Strong transcription	Left Ventricle	heart
44	chr6:161514600-161541000	Strong transcription	Fetal Intestine Large	intestine
45	chr6:161515000-161521000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:161515200-161520600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:161515200-161526000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:161515400-161521000	Weak transcription	Fetal Brain Female	brain
49	chr6:161515400-161522600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:161515400-161527600	Weak transcription	Brain Hippocampus Middle	brain

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